Res: [gmx-users] different number of waters (grompp)

[Ricardo O. S. Soares]

Ricardo O. S. Soares wrote:
> Hello dear users,
> 
> I'm having a problem trying to simulate one trimer. I'm using tip4p water and 
>right after I fill the box with water and try to pre-process (grompp) the 
>resulting .gro and .top, I get the following error:
> 
> 
> -------------------------------------------------------
> Program grompp, VERSION 4.5.1
> Source code file: grompp.c, line: 377
> 
> Fatal error:
> number of coordinates in coordinate file (../box/box_water.gro, 274045)
>              does not match topology (../top_water.top, 273029)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> 
> Here's the ending of the .top file:
> 
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> Protein_chain_H     1
> Protein_chain_L     1
> SOL                59
> SOL                97
> SOL                98
> SOL             66032
> 
> And the beginning of the .gro file shows the number "274045"
> 
>
>
>>The .top specifies fewer atoms than the .gro, so it's possible that there was 
>>some problem when genbox wrote the topology.  The screen output of genbox should 
>>>>have indicated how many waters were added - does this number match what you 
>>see in the .top?  Presumably the first three SOL entries are crystal waters?  I 
>>>>don't know  that pre-existing waters should cause any problem, but it's 
>>possible.  The difference in the number of atoms is 1016, or 254 TIP4P 
>>molecules. 
>>

Before updating to 4.5.4, I removed the crystal waters from the pdb file and now 
the grompp went fine. The problem was probably the different water notations 
after the genbox step. Here follows an exemple:

Crystal water before (original pdb):
...
HETATM 3999  O   HOH A 410      24.263  -7.517 -15.541  1.00 27.99           O  
HETATM 4000  O   HOH A 411       5.682    7.359   2.277  1.00 35.66           O  

HETATM 4001  O   HOH A 412      20.924   0.175 -18.311  1.00 30.25           O  
HETATM 4002  O   HOH A 413       7.366   3.959  -6.173  1.00 36.77           O  
HETATM 4003  O   HOH A 414       0.563  16.043  -5.418  1.00 29.62           O   

...
and the added tip4p waters:
...
  121SOL     OW 1760   0.519   0.692   0.680
  121SOL    HW1 1761   0.504   0.612   0.731
  121SOL    HW2 1762   0.601   0.727   0.714
  121SOL     MW 1763   0.527   0.684   0.692
  122SOL     OW 1764   0.856   1.378   1.365
...

I just wonder if the romoval of these crystal water may introduce artifacts to 
the simulation.

Thanks for your insights!


>>Coincidentally, 59 + 97  + 98 = 254.  It looks like genbox wrote the wrong 
>>number  of molecules it added.  If this is the case, please file an issue on 
>>>>redmine.gromacs.org with the exact steps  taken to reproduce the problem so it 
>>can be fixed.
>>
>>-Justin
>
> Thanks for your time.
> 
> Ricardo.
> 

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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